[gmx-users] Umbrella Sampling-gmx distance
rose rahmani
rose.rhmn93 at gmail.com
Thu Jan 11 15:50:30 CET 2018
still like this
# This file was created Thu Jan 11 09:46:46 2018
# Created by:
# :-) GROMACS - gmx distance, VERSION 5.1.4 (-:
#
# Executable: /usr/local/gromacs/bin/gmx
# Data prefix: /usr/local/gromacs
# Command line:
# gmx distance -n index.ndx -f conf0.gro -oxyz dist0.xvg
# gmx distance is part of G R O M A C S:
#
#
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#
@ title "Distance"
@ xaxis label "Time (ps)"
@ yaxis label "Distance (nm)"
@TYPE xy
0.000 0.192 0.270 0.191 -0.192 -0.270 0.191 0.383
0.000 0.000 0.383 0.000 0.000 0.383 0.000 0.000
0.383 0.000 0.000 1.131 0.270 0.191 0.382 0.000
0.000 0.382 0.000 0.000 0.383 0.000 0.000 0.383
0.000 0.000 0.383 0.000 0.000 0.383 0.000 0.000
0.383 0.000 0.000 0.382 0.000 0.000 0.748 -0.270
0.191 0.382 0.000 0.000 0.382 0.000 0.000 0.382
0.000 0.000 0.382 0.000 0.000 0.000 0.541 0.000
0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
0.541 0.000 0.000 0.541 0.000 0.192 0.270 0.191
-0.192 -0.270 0.191 0.383 0.000 0.000 0.383 0.000
0.000 0.383 0.000 0.000 0.383 0.000 0.000 1.131
0.270 0.191 0.382 0.000 0.000 0.382 0.000 0.000
0.383 0.000 0.000 0.383 0.000 0.000 0.383 0.000
0.000 0.383 0.000 0.000 0.383 0.000 0.000 0.382
0.000 0.000 0.748 -0.270 0.191 0.382 0.000 0.000
0.382 0.000 0.000 0.382 0.000 0.000 0.382 0.000
0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
0.000 0.000 0.541 0.000 0.000 0.
On Thu, Jan 11, 2018 at 4:40 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 1/11/18 3:43 AM, rose rahmani wrote:
>
>> Hi
>>
>> i'm doing umbella sampling. whenever i use gmx distance after pulling in
>> V.5.1.4 , i wouldn't have proper dist.xvg file.for example; this my mdp
>> file for pulling:
>>
>> integrator = md
>> dt = 0.001
>> nsteps = 2500000
>> nstxout = 5000
>> nstvout = 5000
>> nstfout = 500
>> nstlog = 500
>> nstenergy = 1000
>> nstxtcout = 1000
>> nstlist = 10
>> rlist = 1.5
>> cutoff_scheme = group
>> coulombtype = pme
>> rcoulomb = 1.5
>> vdwtype = Switch
>> rvdw_switch = 1.0
>> rvdw = 1.2
>> pcoupl = no
>> gen_vel = no
>> constraints = h-bonds
>> ns_type = grid
>> pbc = xy
>> freezegrps = WAL ZnS
>> freezedim = Y Y Y Y Y Y
>> energygrp-excl = WAL WAL ZnS ZnS
>> energygrps = SOL WAL ZnS Protein NA CL
>> nwall = 2
>> wall-atomtype = C C
>> wall-type = 9-3
>> wall-density = 150 150
>> wall-ewald-zfac = 3
>> ewald-geometry = 3dc
>> fourierspacing = 0.12
>> tcoupl = v-rescale
>> tc-grps = System
>> tau-t = 0.1
>> ref-t = 300
>>
>> ; Pull code
>> pull = yes
>> pull_ngroups = 2
>> pull_ncoords = 1
>> pull_group1_name = ZnS
>> pull_group2_name = Protein
>> pull_coord1_type = umbrella
>> pull_coord1_geometry = direction
>> pull_coord1_groups = 1 2
>> pull_coord1_dim = N N Y
>> pull_coord1_vec = 0 0 1
>> pull_coord1_rate = -0.001
>> pull_coord1_k = 5000
>> pull_coord1_start = yes
>> pull_nstxout = 10
>>
>>
>> and this is dist0.xvg
>>
>> # This file was created Thu Jan 11 03:19:07 2018
>> # Created by:
>> # :-) GROMACS - gmx distance, VERSION 5.1.4 (-:
>> #
>> # Executable: /usr/local/gromacs/bin/gmx
>> # Data prefix: /usr/local/gromacs
>> # Command line:
>> # gmx distance -s pull.tpr -n index.ndx -f conf0.gro -oall dist0.xvg
>>
>
> By using -oall, you're getting a matrix of all distances between the atoms
> in the selected groups. You just want a COM distance, so you need -oxyz
> with a suitable COM selection (see http://manual.gromacs.org/docu
> mentation/2018-latest/user-guide/cmdline.html#g-dist)
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
> --
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